import of KGML file seems bugged

[karchern]

Hi,

thanks for the incredibly useful tool!

For some pathways, it seems that keggscape (the cytocape plugin) is bugged?

For example, If I try to import the attached KEGG pathway xml (bvu00300 exported/downloaded from KEGG as explained in the keggscape tutorial), the imported pathway is incomplete. I'm attaching the xml file (I had to rename it to .txt since .xml file upload seems prohibited.

See below for screenshot; the bottom left part lacks a lot of edges that are evidently part of the pathway and also clearly visible in KEGG.

I am using Cytoscape version 3.10.3, keggscape version v0.9.2 on an M1 Mac.

[kozo2]

As you can see by viewing the 'bvu00300.xml' text with any editor, that XML does not contain edge information for nodes without gene annotations.

The current KEGGscape is designed to visualize the XML information as it is, which is why it's displayed that way.

If you have any ideas on what kind of changes you would like to see, please let me know.